We studied the dynamic behavior of red shifted mutants of the fluorescence of green fluorescent protein (GFP) like S65T and EGFP by FCS and discovered a fast blinking effect dependent on the pH of the used buffer. This indicates that the protein spends a considerable amount of time in a dark state, with transitions back and forth to the bright state on the 100 ?s time scale. The findings can be related to the overall fluorescence that decreases at low pH. Structural knowledge about this protein suggests that the dark state is actually a protonated form of the chromophore that shifts the absorption to smaller values where no excitation by the FCS laser can occur. FCS thus allows to derive precise kinetic and thermodynamic information of this reversible protonation process.